UltraClean Plant RNA Isolation Kit

UltraClean Plant RNA Isolation Kit Catalog No. Quantity 13300-20 20 Preps 13300-50 50 Preps Instruction Manual For support contact: 306, Aggarwal City Mall, Opposite M2K Pitampura, Delhi India 110034 Contact: (INDIA). Ph: +91-11-42208000, 42208111, 42208222 Mobile: +91-9810521400 Fax: +91-11-42208444 Life Technologies (India) Pvt. Ltd. Email: customerservice@atzlabs.com 306, Aggarwal City Mall, Opposite M2K Pitampura, Web: www.atzlabs.com Delhi 110034 (INDIA). Ph: +91-11-42208000, 42208111, 42208222 Mobile: +91-9810521400 Fax: +91-11-42208444 Email: customerservice@lifetechindia.com Web: www.lifetechindia.com Please recycle Version: 06192009 1

Table of Contents Introduction... 3 Protocol Overview... 3 Equipment Required... 4 Kit Contents & Storage... 4 Precautions & Warnings... 4 Important Notes Before Starting... 5 Suggested Protocol for Formaldehyde Agarose Gel Electrophoesis... 7 Protocol...8 Hints & Troubleshooting Guide...9 Contact Information...10 Other Quality Products Available...11 2

Introduction The UltraClean Plant RNA Isolation Kit is designed to isolate total RNA from a wide variety of plant materials. Sample sizes from 5 to 100 mg can be processed for up to 60 g of RNA. All contaminants, such as polysaccharides, are removed, and the eluted RNA is ready for all downstream applications. Protocol Overview Fresh or frozen plant tissues are homogenized using standard manual methods. After cell lysis, the released RNA is captured on a silica membrane spin filter. The RNA bound to the filter is washed to remove all contaminants. Finally, the RNA is recovered in certified RNase-free water (provided). The eluted RNA is ready for all downstream applications including reverse transcription (RT) and reverse transcription PCR (RT-PCR). This kit is for research purposes only. Not for diagnostic use. Other Related Products Catalog No. Quantity UltraClean Lab Cleaner 12095-250 12095-500 12095-1000 RNase-Free Gloves 1555-XS 1555-S 1555-M 1555-L DEPC Treated Water 17011-200 17011-5200 250 ml squeeze bottle 500 ml spray bottle 1 liter bottle Bag of 100 Bag of 100 Bag of 100 Bag of 100 200 ml 5 x 200 ml 3

Equipment Required Homogenizer (see notes on homogenization) Microcentrifuge (10,000 x g) Pipettor (volumes required 5 l - 1000 l) Kit Contents Kit Catalog# 13300-20 Kit Catalog# 13300-50 Component Catalog# Amount Catalog# Amount Solution PMR1 13300-20-1A 25 ml 13300-50-1A 60 ml Solution PMR2 13300-20-2A 12 ml 13300-50-2A 30 ml Solution PMR3 13300-20-3A 8 ml 13300-50-3A 15 ml Solution PMR4 13300-20-4A 20 ml 13300-50-4A 2 x 25 ml Solution PMR5 13300-20-5A 15 ml 13300-50-5A 30 ml Solution PMR6 13300-20-6A 2 ml 13300-50-6A 5 ml Spin Filter Units in 2 ml Tubes 13300-20-SF 20 13300-50-SF 50 2 ml Collection Tubes 13300-20-T 80 13300-50-T 200 Kit Storage Kit reagents and components should be stored at room temperature (15-30 C). Note: If solution PMR1 falls out of solution, heat the bottle before using this solution. Precautions Please wear gloves when using this product. Avoid all skin contact with kit reagents. In case of contact, wash thoroughly with water. Do not ingest. See Material Safety Data Sheets for emergency procedures in case of accidental ingestion or contact. All MSDS information is available upon request (760-929- 9911) or at www.mobio.com. Reagents labeled flammable should be kept away from open flames and sparks. WARNING: Solution PMR5 and PMR4 are flammable. To avoid injury or fire keep, away from open flames and sparks. IMPORTANT NOTE FOR USE: Make sure all tubes rotate freely in your centrifuge without rubbing. 4

Important Notes Before Starting Information Isolation of biologically intact RNA is an essential step in many types of biochemical investigations, including the cloning and quantification of reverse-transcribed mrnas through RT-PCR. The yield and quality of RNA obtained varies with the amount, type of tissues and the age of tissues used. Tissue Preparation Chop plant material into small pieces. Smaller pieces will homogenize more efficiently. Young and fresh tissues are ideal for isolating RNA. It has been reported widely in the literature that the content of polyphenols increases with plant age and it is easier to isolate RNA from young plant tissues. The quality of RNA is affected by compounds extracted along with nucleic acids, particularly polyphenols and their quinone oxidation products, and polymeric carbohydrates from the cell wall and middle lamella. During the homogenization process cells are disrupted leading to the oxidation of phenolic compounds which can then interact irreversibly with proteins and nucleic acids (Dimick and Hoskin, 1981). These substances which bind to nucleic acids inhibit translational activity of RNA (Callahan et al. 1989) and interfere with the quantitation of total DNA and RNA by UV absorption (Newbury and Possingham, 1977). Thus, it is essential to consider the age and type of plant tissues processed before starting with the isolation of RNA. Amount of Starting Material We do recommend the use of up to 100 mg of tissue samples as the starting materials in 1 ml of lysis buffer PMR1. Exceeding 100 mg/ml of the lysis buffer will reduce the efficiency of the kit and may result in problems such as increased genomic DNA contamination, clogging of the spin filters, degradation of RNA and excess foaming during homogenization. Homogenization Note: When homogenizing plant material rotate tube. This will cause the probe to pop any bubbles or foam that accumulate. The UltraClean Plant RNA Isolation Kit is optimized using Polytron as the homogenizer. The ideal speed setting is # 5 and the homogenization time is 90 seconds. Shorter homogenization time reduces the RNA yield while increasing contamination with high molecular genomic DNA. Homogenizing the tissues for 90 seconds effectively shears the DNA and improves the RNA yield significantly. Tissues can be homogenized conveniently, without the problem of splashing or foaming out the tubes, by the use of 10 or 15 ml tubes. The use of 10 ml tubes with a flat bottom is recommended for efficient homogenization when a polytron is used. The use of handheld homogenizers such as PRO 200 can also be used to homogenize the tissue samples. Some plant types such as onion shoots will foam even in a 10 or 15 ml tube, and for these samples, the homogenization time should be reduced to 60 seconds or the starting material should be reduced to 50 mg/ml of lysis buffer. Tissue Types and Amount to Process Table 1. Tissue Types Optimal Amount to Process Expected Yield ( g) Spinach leaves 100 mg 15 Onion shoots 100 mg 7 Cauliflower leaves 100 mg 10 Broccoli leaves 100 mg 4 Radish leaves 100 mg 10 Corn leaves 100 mg 20 Sunflower leaves 100 mg 9 Wheat grass blades 100 mg 20 5

Processing Frozen Tissue If frozen and using a mortar and pestle, the tissue should never be allowed to thaw during maceration and should be completely crushed to a fine powder in a mortar and pestle that is compatible with liquid nitrogen before adding the lysis buffer. Mix thoroughly to assure full lysis of the cells and allow the lysis buffer to denature proteins and free the nucleic acids for isolation and purification. Please keep in mind that tissues must be lysed and the genomic DNA homogenized in the most efficient manner to isolate the greatest amount of RNA. The binding capacity of the spin filter must not be exceeded or this may affect your ability to bind all the available RNA (up to 20 g). 6

Suggested Protocol for Formaldehyde Agarose Gel Electrophoresis Solutions needed. 10x Formaldehyde Agarose gel buffer 200 mm 3-[N-morpholino] propanesulfonic acid (MOPS) (free acid) 50 mm Sodium Acetate 10 mm EDTA ph to 7.0 with Sodium Hydroxide. 1x Formaldehyde Agarose gel buffer (1L) 100 ml 10x Formaldehyde Agarose gel buffer 20 ml 37% (12.3M) Formaldehyde 880 ml DEPC treated water 5x RNA Loading Dye 16 l Saturated aqueous Bromophenol blue solution 80 l 0.5 M EDTA, ph 8.0 720 l 37% (12.3M) Formaldehyde 2 ml 100% Glycerol 3084 l Formamide 4 ml 10x Formaldehyde Agarose gel buffer Formaldehyde Agarose Gel preparation To make a 1.2% formaldehyde agarose gel with 100 ml volume mix the following: 1.2 g Agarose 10 ml 10x Formaldehyde Agarose gel buffer 90 ml DEPC treated water Heat the mixture in a microwave oven to melt the agarose. Cool to 65 C in a waterbath. Add 1.8 ml 37% (12.3M) Formaldehyde and 2 l of 5 mg/ml Ethidium Bromide. Swirl to mix and pour into a gel box. The gel must be pre-ran for 30 minutes in 1x Formaldehyde Agarose gel buffer before loading the samples. RNA Sample Preparation The eluted RNA samples must be denatured before running on a formaldehyde agarose gel. To the sample to be loaded, add 1 volume of 5x RNA loading dye for each 4 volumes of RNA sample i.e. 2 l of 5x RNA loading dye for each 8 l of RNA sample. Mix the samples well and use a picofuge to collect the sample at the bottom of the tube. Incubate at 65 C for 3-5 minutes, then chill on ice and load in the Formaldehyde agarose gel. Run the gel at 5-7 V/cm in 1x Formaldehyde Agarose gel buffer. References 1. Callahan, A., Morgens, P., and Walton, E. 1989. Hortic. Sci. 24: 356-358. 2. Dimick, P.S., and Hoskin, J.M. 1981. Can. Inst. Food Sci. technol. J. 14: 269-282. 3. Newbury, H.J., and Possingham, J.V. 1977. Plant Physiol. 60: 543 547. 7

Protocol Please wear RNase-Free gloves at all times. MO BIO RNase-Free Gloves Catalog#: 1555-S (small), 1555-M (medium), 1555-L (large) 1. Homogenize up to 100 mg of tissues in 1 ml of PMR1. NOTE: Shake the bottle several times before dispensing PMR1. If the solution precipitates, heat the bottle to 65 C and dissolve the precipitates, shake the bottle and then dispense PMR1. Check for precipitates before using. See Important Information for details about homogenizing different tissue types and amounts to use Table 1. 2. Transfer the homogenate to a 2 ml Collection Tube (provided). 3. Centrifuge at 10,000 x g for 3 minutes. 4. Transfer 600 l of the clear homogenate to a new 2 ml Collection Tube (provided). NOTE: Depending upon the tissue type, you may have varying amounts of the lysate. However, you should have at least 600 l. It is strongly suggested to take not more than 600 l of the lysate without disturbing the pellet. With some plant type, it will be a loose pellet and a minimum of plant debris carried over will not affect the protocol. 5. Add 500 l of PMR2. 6. Add 250 l of PMR3. 7. Invert the tubes five times to mix. 8. Incubate on ice for 5 minutes. 9. Centrifuge the tubes for 10 minutes at 10,000 x g. 10. Avoiding the pellet, transfer the entire volume of supernatant to a clean 2 ml Collection Tube (provided). You can expect approximately 1000 l in volume. NOTE: It is important not to disturb the pellet in order to ensure a smooth flow-through the spin filters. It is safer not to use a pipette tip for this step, instead transfer directly by inverting the supernatant into the 2 ml Collection Tube. 11. Add 800 l of PMR4 to the supernatant, pipette up and down to mix. 12. Load about 650 l into Spin Filter and centrifuge at 10,000 x g for 30 seconds. Discard the flow through and add the remaining supernatant to the spin filter and centrifuge at 10,000 x g for 30 seconds. NOTE: A total of 3 loads for each sample processed are required. Discard all flow through liquid. If clogging occurs, you may have used too much tissue or the homogenization step was incomplete. See important information page to determine appropriate amounts of tissue to process. You may need to cut back on the amount of tissue used even if the amount you tried falls within the guidelines described. 13. Add 500 l of PMR5 and centrifuge for 30 seconds at 10,000 x g. 14. Discard the flow through. 15. Centrifuge again for 1 minute to remove the residual wash solution. 16. Being careful not to splash liquid on the filter basket, place spin filter basket in a new 2 ml Collection Tube (provided). 17. Add 50 l of PMR6 (RNase-Free Water) to the center of the white filter membrane. 18. Centrifuge 30 seconds. 19. Discard Spin Filter. RNA in the tube may contain some amount of DNA. Digestion with RNase-Free DNase may be necessary. We recommend storing RNA frozen (-20 C or -80 C). (RNase-Free Water) contains no EDTA. Thank you for choosing the UltraClean Plant RNA Isolation Kit 8

Hints and Troubleshooting Guide Concentrating the RNA Your final volume will be 50 l. If this is too dilute for your purposes, add 5 l of 3M NaAcetate and mix. Then add 150 l of 100% cold ethanol. Mix, and incubate at -70 C for 15 minutes or -20 C for 2 hours to overnight. Centrifuge at 10,000 x g for 10 minutes at 4 C. Decant all liquid. Briefly dry residual ethanol in a speed vac or ambient air. Do not over-dry pellet or resuspension may be difficult. Resuspend precipitated RNA in desired volume of RNase-Free Water. RNA Floats Out of Well When Loaded on a Gel You may have inadvertently transferred residual solution TR5 to the final sample. Prevent this by being careful in step 11 not to transfer liquid onto the bottom of the spin filter basket. Ethanol precipitation is the best way to remove residual solution PMR5. (See concentrating RNA above) Storing RNA RNA is eluted in RNase-Free Water and should be used immediately or stored at -20 C or it may degrade. RNA should be precipitated in EtOH and stored at -20 C to ensure minimal degradation during long term storage. Spin Filter Clogging When the concentration of tissues processed exceed 30 mg/600 l, the spin filters are likely to clog. If this happens, the centrifugation time should be increase from 30 seconds to 2 minutes. If the problem persists, then the lysate should be diluted with 100% PMR4, usually by adding an equal volume of 100% PMR4. DNase Digestion This kit will isolate RNA that in most cases is free of genomic DNA. However, if you plan to do Reverse transcription reactions or RT PCR, we highly recommend that you treat your RNA with DNase prior to proceeding. Be sure the DNase you plan to use is certified RNase-Ffree or you may lose or degrade your RNA sample. You can purchase RNase free DNase from MO BIO Laboratories Catalog# 15600-5. To order contact: 306, Aggarwal City Mall, Opposite M2K Pitampura, Delhi 110034 (INDIA). Ph: +91-11-42208000, 42208111, 42208222 Mobile: +91-9810521400 Fax: +91-11-42208444 Email: customerservice@atzlabs.com Web: www.atzlabs.com 9